Time-varying overdispersion of SARS-CoV-2 transmission during the periods when different variants of concern were circulating in Japan.

Japan has implemented a cluster-based approach for coronavirus disease 2019 (COVID-19) from the pandemic's beginning based on the transmission heterogeneity (overdispersion) of severe acute respiratory coronavirus 2 (SARS-CoV-2). However, studies analyzing overdispersion of transmission among new variants of concerns (VOCs), especially for Omicron, were limited. Thus, we aimed to clarify how the transmission heterogeneity has changed with the emergence of VOCs (Alpha, Delta, and Omicron) using detailed contact tracing data in Yamagata Prefecture, Japan. We estimated the time-varying dispersion parameter ([Formula: see text]) by fitting a negative binomial distribution for each transmission generation. Our results showed that even after the emergence of VOCs, there was transmission heterogeneity of SARS-CoV-2, with changes in [Formula: see text] during each wave. Continuous monitoring of transmission dynamics is vital for implementing appropriate measures. However, a feasible and sustainable epidemiological analysis system should be established to make this possible.

Measles Outbreak Response Activity in Japan, and a Discussion for a Possible Strategy of Outbreak Response Using Cycle Threshold Values of Real-Time Reverse Transcription PCR for Measles Virus in Measles Elimination Settings.

Measles is a highly contagious, but vaccine-preventable disease caused by the measles virus (MeV). Although the administration of two doses of measles vaccines is the most effective strategy to prevent and eliminate measles, MeV continues to spread worldwide, even in 2022. In measles-eliminated countries, preparedness and response to measles outbreaks originating from imported cases are required to maintain elimination status. Under these circumstances, real-time reverse transcription (RT) PCR for MeV could provide a diagnostic method capable of strengthening the subnational capacity for outbreak responses. Real-time RT-PCR can detect MeV RNA from patients with measles at the initial symptomatic stage, which can enable rapid public health responses aimed at detecting their contacts and common sources of infection. Furthermore, low cycle threshold (Ct) values (i.e., high viral load) of throat swabs indicate high infectiousness in patients with measles. The high basic reproduction number of measles suggests that patients with high infectiousness can easily become super-spreaders. This opinion proposes a possible strategy of rapid and intensive responses to counter measles outbreaks caused by super-spreader candidates showing low Ct values in throat swabs. Our strategy would make it possible to effectively prevent further measles transmission, thereby leading to the early termination of measles outbreaks.

Epidemiology of Coronavirus Disease 2019 in Yamagata Prefecture, Japan, January-May 2020: the Importance of Retrospective Contact Tracing.

Public health interventions have played an important role in controlling coronavirus disease 2019 (COVID-19), which is a rapidly spreading infectious disease. To contribute to future COVID-19 countermeasures, we aimed to verify the results of the countermeasures employed by public health centers (PHCs) against the first wave of COVID-19 in Yamagata Prefecture, Japan (Yamagata). Between January and May 2020, 1,253 patients suspected of SARS-CoV-2 infection were invited for testing. Simultaneously, based on retrospective contact tracings, PHCs investigated the infection sources and transmission routes of laboratory-confirmed COVID-19 cases and tested 928 contacts. Consequently, 69 cases were confirmed between March 31 and May 4, 58 of whom were from among the contacts (84.1%; 95% confidence interval [CI] 75.5-92.7). The spread of infection was triggered in cases harboring epidemiological links outside Yamagata. Subsequently, the number of cases rapidly increased. However, PHCs identified epidemiological links in 61 (88.4%; 95% CI 80.8-96.0) of the 69 cases, and transmission chains up to the fifth generation. Finally, the spread of infection ended after approximately one month. Our results indicate that the identification of infection sources and active case finding from contacts based on retrospective contact tracing was likely to be an effective strategy in ending the first wave of COVID-19 in Yamagata.

The Largest Measles Outbreak, Including 38 Modified Measles and 22 Typical Measles Cases in Its Elimination Era in Yamagata, Japan, 2017.

The incidence of modified measles (M-Me), characterized by milder symptoms than those of typical measles (T-Me), has been increasing in Japan. However, the outbreak dominated by M-Me cases has not been thoroughly investigated worldwide. The largest importation-related outbreak of measles with genotype D8 occurred in Yamagata Prefecture, Japan, from March to April 2017. This phenomenon was observed after Japan had achieved measles elimination in 2015. We confirmed 60 cases by detecting the genome of the measles virus (MeV). Among the cases, 38 were M-Me and 22 were T-Me. Thirty-nine (65.0%) patients were 20-39 years of age. Three out of 7 primary cases produced 50 transmissions, of which each patient caused 9-25 transmissions. These patients were 22-31 years old and were not vaccinated. Moreover, they developed T-Me and kept contact with the public during their symptomatic periods. Considering that M-Me is generally caused by vaccine failure, some individuals in Japan may have insufficient immunity for MeV. Accordingly, additional doses of measles vaccine may be necessary in preventing measles importation and endemicity among individuals aged 20-39 years. Furthermore, to accurately and promptly diagnose individuals with measles, particularly those who can be considered as primary cases, efforts must be exerted to detect all measles cases using epidemiological and genetic approaches in countries where measles elimination had been achieved.

Convenient PCR method for variable-number tandem-repeat typing of Mycobacterium tuberculosis clinical isolates.

Variable-number tandem-repeat typing for Mycobacterium tuberculosis clinical isolates contributes to evidence-based tuberculosis control. However, cumbersome PCR procedures for the typing have disturbed routine analyses. We proposed a convenient PCR method for the typing using a PCR master mix that provides rapidity and long-term stability of the frozen PCR cocktail.

Mycobacterium tuberculosis Transmission among Elderly Persons, Yamagata Prefecture, Japan, 2009-2015.

In many countries with low to moderate tuberculosis (TB) incidence, cases have shifted to elderly persons. It is unclear, however, whether these cases are associated with recent Mycobacterium tuberculosis transmission or represent reactivation of past disease. During 2009-2015, we performed a population-based TB investigation in Yamagata Prefecture, Japan, using in-depth contact tracing and 24-loci variable-number tandem-repeat typing optimized for Beijing family M. tuberculosis strains. We analyzed 494 strains, of which 387 (78.3%) were derived from elderly patients. Recent transmission with an epidemiologic link was confirmed in 22 clusters (70 cases). In 17 (77.3%) clusters, the source patient was elderly; 11 (64.7%) of the 17 clusters occurred in a hospital or nursing home. In this setting, the increase in TB cases was associated with M. tuberculosis transmissions from elderly persons. Prevention of transmission in places where elderly persons gather will be an effective strategy for decreasing TB incidence among predominantly elderly populations.

[COMPARISON OF QuantiFERON® TB GOLD TEST RESULTS BEFORE AND AFTER ENDOTOXIN CONTAMINATION].

PURPOSE: In response to a case of endotoxin contamination of tubes used in QuantiFERON® TB Gold (QFT-3G) testing in Japan in 2013, the effect of this contamination on QFT-3G test results was investigated. METHODS: We analyzed QFT-3G results from 4,258 participants in a tuberculosis contact investigation in Yamagata, Japan from September 2010 to April 2015. Of these, 2,488 samples were collected before the endotoxin contamination, while 1,770 samples were collected after the contamination. RESULTS: Negative control values in the group tested after the contamination were significantly lower than those in the group tested before the contamination (P < 0.0005). The proportion of positive controls that exceeded the calculated limit (10IU/ml) in the group tested after the contamination (87.8%) was lower than that in the group tested before the contamination (96.8%; P < 0.0005). The proportion of intermediate results in the group tested after the contamination (3.2%) was markedly lower than that in the group tested before the contamination (6.6%). DISCUSSION: Differences in QFT-3G test results were found to be related to a difference in blood collection before or after endotoxin contamination of blood collection tubes. Values resulting from QFT-3G testing were lower in blood samples that were collected after the contamination relative to those collected before the contamination.

Phylogenetic assignment of Mycobacterium tuberculosis Beijing clinical isolates in Japan by maximum a posteriori estimation.

Intra-species phylogeny of Mycobacterium tuberculosis has been regarded as a clue to estimate its potential risk to develop drug-resistance and various epidemiological tendencies. Genotypic characterization of variable number of tandem repeats (VNTR), a standard tool to ascertain transmission routes, has been improving as a public health effort, but determining phylogenetic information from those efforts alone is difficult. We present a platform based on maximum a posteriori (MAP) estimation to estimate phylogenetic information for M. tuberculosis clinical isolates from individual profiles of VNTR types. This study used 1245 M. tuberculosis clinical isolates obtained throughout Japan for construction of an MAP estimation formula. Two MAP estimation formulae, classification of Beijing family and other lineages, and classification of five Beijing sublineages (ST11/26, STK, ST3, and ST25/19 belonging to the ancient Beijing subfamily and modern Beijing subfamily), were created based on 24 loci VNTR (24Beijing-VNTR) profiles and phylogenetic information of the isolates. Recursive estimation based on the formulae showed high concordance with their authentic phylogeny by multi-locus sequence typing (MLST) of the isolates. The formulae might further support phylogenetic estimation of the Beijing lineage M. tuberculosis from the VNTR genotype with various geographic backgrounds. These results suggest that MAP estimation can function as a reliable probabilistic process to append phylogenetic information to VNTR genotypes of M. tuberculosis independently, which might improve the usage of genotyping data for control, understanding, prevention, and treatment of TB.

Clonality and micro-diversity of a nationwide spreading genotype of Mycobacterium tuberculosis in Japan.

Mycobacterium tuberculosis transmission routes can be estimated from genotypic analysis of clinical isolates from patients. In Japan, still a middle-incidence country of TB, a unique genotype strain designated as 'M-strain' has been isolated nationwide recently. To ascertain the history of the wide spread of the strain, 10 clinical isolates from different areas were subjected to genome-wide analysis based on deep sequencers. Results show that all isolates possessed common mutations to those of referential strains. The greatest number of accumulated single nucleotide variants (SNVs) from the oldest coalescence was 13 nucleotides, indicating high clonality of these isolates. When an SNV common to the isolates was used as a surrogate marker of the clone, authentic clonal isolates with variation in a reliable subset of variable number of tandem repeat (VNTR) genotyping method can be selected successfully from clinical isolates populations of M. tuberculosis. When the authentic clones can also be assigned to sub-clonal groups by SNVs derived from the genomic comparison, they are classifiable into three sub-clonal groups with a bias of geographical origins. Feedback from genomic analysis of clinical isolates of M. tuberculosis to genotypic markers will be an efficient strategy for the big data in various settings for public health actions against TB.

[Effectiveness of interferon-gamma release assays in the tuberculosis contact investigation of elderly people].

PURPOSE: To confirm the effectiveness of interferon-gamma release assays (IGRAs) in the tuberculosis (TB) contact investigation of elderly people, we analyzed the results of the QuantiFERON TB Gold in tube (QFT-3G) test, which is a commercially available IGRA. METHODS: We analyzed the results of the QFT-3G test in 2,420 subjects who were in close contact with TB patients. We investigated subjects with latent TB infection and those showing the onset of TB among the QFT-3G-positive subjects. RESULTS: The QFT-3G-positive rate was 7.3% (95% confidence interval, 6.2%-8.3%). In addition, we demonstrated that the QFT-3G-positive rate increased with age (P < 0.001). DISCUSSION: The QFT-3G-positive rate was high, particularly in elderly people (> or = 60 years), but the rate was significantly lower than the predicted prevalence of TB infection. Therefore, it was assumed that the QFT-3G test does not always provide a positive result, even in cases of subjects with a previous TB infection. Furthermore, data from the QFT-3G-positive subjects indicated that approximately one half of subjects aged 60-69 years, approximately one-third of those aged 70-79 years, and approximately one-quarter of those aged over 80 years have had recent TB infections. In conclusion, the results of the QFT-3G test in elderly people need to be carefully evaluated according to the contact situation with TB patients; nevertheless, the QFT-3G test is useful for the screening of latent TB infection in elderly people who were in close contact with TB patients.

[Effectiveness of comprehensive variable number of tandem repeat (VNTR) analysis in areas with a low incidence of tuberculosis].

PURPOSE: To ascertain the effectiveness of variable number of tandem repeat (VNTR) analysis in areas with a low incidence of tuberculosis (TB), we examined the combination of comprehensive VNTR analyses and field epidemiological investigation results in Yamagata Prefecture, Japan, where estimated incidence of new TB cases per 100,000 population was 11.3 in 2011. METHODS: We collected Mycobacterium tuberculosis isolates from 184 (69.2%) of 266 pulmonary TB patients across the whole of Yamagata Prefecture between 2009 and 2011. Next, 24 loci [JATA (12), QUB-11a, ETR A, QUB-18, QUB3232, v3820, v4120, MIRU04, MIRU16, MIRU40, ETR C, Mtub30, Mtub39] in VNTR genotypes were determined. The relationships among TB patients derived from the respective clusters were surveyed using field epidemiological investigation results provided by the Public Health Center. RESULTS: Seventeen clusters were formed by 49 (26.6%) of the 184 isolates. We found 3 hospital infection cases, 3 family infection cases, and 1 nursing home infection case forming 6 clusters. Among these cases, two relationships among patients were revealed after additional epidemiological investigation at the Public Health Center. The VNTR pattern of the largest cluster, which was formed by 12 isolates, was identical with that of an incipient patient of a TB mass infection that occurred in 2007. DISCUSSION: In areas with a low incidence of TB, a combination of comprehensive VNTR analysis and field epidemiological investigation is useful to find unknown transmission routes, identify for new risk groups, and trace mass infections.

Epidemic myalgia associated with human parechovirus type 3 infection among adults occurs during an outbreak among children: findings from Yamagata, Japan, in 2011.

BACKGROUND: Based on our findings in Yamagata, Japan, in 2008, we reported that human parechovirus type 3 (HPeV3) could be associated with epidemic myalgia among adults, although HPeV3 is generally associated with infectious diseases in children. OBJECTIVES: To clarify the relationship between community outbreaks among children and myalgia through the continued surveillance of HPeV3 infections. STUDY DESIGN: In the summer season (June-August) of 2011, we collected 586 specimens from children with infectious diseases, and throat swabs, and stool and serum specimens from 5 patients with myalgia. We detected HPeV3 using virus isolation and reverse-transcription PCR, and carried out phylogenetic analysis. We also performed screening for HPeV3 using 309 stocked frozen specimens collected in 2008 for a comparison between 2008 and 2011 strains. RESULTS: We detected HPeV3 in 59 children and isolated HPeV3 from all myalgia patients. Phylogenetic analysis indicated that the HPeV3 strains circulating in 2008 and 2011 could be clearly distinguished, apart from two strains. Further, we detected HPeV3 strains with identical nucleotide sequences from children and adults in 2008 and 2011, respectively. Two children belonging to one myalgia patient had upper respiratory infections prior to the onset of their father's illness, and the HPeV3 isolates from these three patients had identical nucleotide sequences. CONCLUSIONS: These findings suggest that HPeV3, circulating among children in the community, infects their household, including parents, a portion of whom may subsequently show symptoms of myalgia. Our observations in 2008 and 2011 strongly suggest that clinical consideration should be given to HPeV3 in children as well as in adults during summer seasons in which an HPeV3 outbreak occurs among the children in the community.

Isolation of vaccine-derived measles viruses from children with acute respiratory infection.

The measles elimination project led by the World Health Organization (WHO) has been moving toward the target of eliminating measles in the WHO Western Pacific Region. In Japan, prefectural public health institutes play a key role for the laboratory diagnosis of measles virus (MV) infection, which is based on PCR, virus isolation, and genotyping. Microscopic examination of viral-sensitive cell lines during routine virus isolation from nasopharyngeal specimens has been used to detect the morphological changes typical for the growth of respiratory viruses. Here, we describe the unexpected isolation of vaccine-derived MVs from the two unrelated 1-year-old boys with acute respiratory infection. The nasopharyngeal specimens were obtained from one patient in February 2007 and from another in December 2012. Incidentally, the two children had received measles-rubella vaccination 9 or 11 days before the sampling. The isolates from two children induced morphological changes of the viral-sensitive cell lines, such as syncythia formation (cell fusion). We finally identified the isolates as vaccine-derived MVs by sequence analysis and immunological methods with anti-measles nucleoprotein antibodies. As no typical symptoms of MV infection were observed in either patient, the vaccine-derived MVs were isolated not as causative pathogens but by chance. In fact, there was no suspected case of secondary MV infection in either patient, thereby excluding the possibility that vaccine-derived MVs spread from human to human. Our experiences suggest the possibility of vaccine-derived MV isolation by cell cultures and the difficulty in identifying MVs in specimens from patients other than clinically suspected measles cases.

Molecular epidemiology of Coxsackievirus A16 strains isolated from children in Yamagata, Japan between 1988 and 2011.

To clarify the longitudinal molecular epidemiology of coxsackievirus A16, phylogenetic analysis based on the VP1 region of 220 isolates in Yamagata, Japan was performed. The resultant phylogenetic tree indicates that the Yamagata isolates and reference strains can be readily genotyped into three genogroups, and 0, 12 and 208 isolates belonged to the first, second, and third genogroups, respectively. The first genogroup includes only the prototype strain, the second strains that had disappeared by the end of the 20th century and the third comprises those that have been circulating since then in local communities, such as Yamagata.

Seasonal patterns of respiratory syncytial virus, influenza A virus, human metapneumovirus, and parainfluenza virus type 3 infections on the basis of virus isolation data between 2004 and 2011 in Yamagata, Japan.

Most acute respiratory infections (ARIs) are thought to be associated with respiratory viruses that cause similar symptoms. Therefore, assessment of clinical and epidemiologic features of these viruses is important for diagnosing a viral infection. We collected 13,325 nasopharyngeal specimens from patients with ARIs and isolated the virus using a microplate method involving 7 cell lines between 2004 and 2011 in Yamagata, Japan. We isolated a total of 5,483 viruses. Respiratory syncytial virus (RSV), influenza A virus (FluA), human metapneumovirus (hMPV), and human parainfluenza virus type 3 (hPIV3) showed clear yearly seasonal patterns; generally, RSV infections peaked at the end of the year, FluA infections peaked between January and March, hMPV infections peaked between March and April, and hPIV3 showed seasonal outbreaks between May and July. Further, RSV, hMPV, and hPIV3 were commonly isolated in 12.0-13.1% of specimens from children aged less than 4 years, whereas FluA was isolated in 7.3-8.2% of specimens from school-aged children. A generalized view of seasonality and age distribution, particularly on the basis of longitudinal epidemiological data, will be helpful for medical decision-making, including decisions related to the use of rapid test kits, selection of antiviral treatments, restriction of antibiotic therapy, and implementation of infection control strategies.

Epidemic myalgia in adults associated with human parechovirus type 3 infection, Yamagata, Japan, 2008.

Human parechovirus has rarely been shown to cause clinical disease in adults. During June-August 2008, a total of 22 adults sought treatment at Yonezawa City Hospital in Yamagata, Japan, for muscle pain and weakness of all limbs; most also had fever and sore throat. All patients received a clinical diagnosis of epidemic myalgia; clinical laboratory findings suggested an acute inflammatory process. Laboratory confirmation of infection with human parechovirus type 3 (HPeV3) was made for 14 patients; we isolated HPeV3 from 7 patients, detected HPeV3 genome in 11, and observed serologic confirmation of infection in 11. Although HPeV3 is typically associated with disease in young children, our results suggest that this outbreak of myalgia among adults was associated with HPeV3 infection. Clinical consideration should be given to HPeV3 not only in young children but also in adults when an outbreak occurs in the community.

Epidemiology of parainfluenza virus types 1, 2 and 3 infections based on virus isolation between 2002 and 2011 in Yamagata, Japan.

To clarify the epidemiology of viral acute respiratory infections (ARIs), 305 human parainfluenza virus types 1 (HPIV1), 154 HPIV2 and 574 HPIV3 strains were isolated from 16,962 nasopharyngeal swabs obtained between 2002 and 2011 at pediatric clinics in Yamagata, Japan. The total isolation frequency for HPIV1-3 was 6.1%. Unlike HPIV1 infections, HPIV3 showed clear seasonality with yearly outbreaks in the spring-summer season. HPIV2 tended to appear biannually in autumn-winter. Although no reliable techniques for the laboratory diagnosis of these infections have been established, the present results suggest that HPIV1-3 are an important causative agent of ARIs in children.